Bruce is forced to undergo surgery to repair the damage to his back. The surgeon-our morphine-addicted doctor-performs the operation. Unfortunately his tools aren't exactly clean. Bruce realizes that he'll have a limited time frame to stop Bane before the infection kills him. So after he escapes the Pit in pain from the infection and he mixes up some of the compound Bane uses to keep his pain at bay.

Batman returns to Gotham. Same stuff happens. The bomb is still there to keep the feds/army at bay. As he's fighting Bane the infection begins to hit him hard. He beats Bane, Talia dies and Batman flies the bomb out of the city. Its not clear if Batman dies in the blast or if he dies from the infection before the bomb goes off.

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"Consistency is the last refuge of the unimaginative." - Oscar Wilde